Setup R notebook Environment
knitr::opts_chunk$set(echo = TRUE)
Sys.setlocale("LC_CTYPE", "en_US.UTF-8")
[1] ""
packages = c("sp","sf","tidyverse","tmap","rjson", "rgdal", "geojsonio", "GISTools",'spatialEco', "raster","dplyr")
for (p in packages){
if(!require(p, character.only = T)){
install.packages(p)
}
library(p,character.only = T)
}
Loading required package: sp
Loading required package: sf
Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: tidyverse
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Loading required package: tmap
Loading required package: rjson
Loading required package: rgdal
rgdal: version: 1.3-6, (SVN revision 773)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
Path to GDAL shared files: C:/Users/terence.tan.2015/Documents/R/win-library/3.5/rgdal/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
Path to PROJ.4 shared files: C:/Users/terence.tan.2015/Documents/R/win-library/3.5/rgdal/proj
Linking to sp version: 1.3-1
Loading required package: geojsonio
Attaching package: <U+393C><U+3E31>geojsonio<U+393C><U+3E32>
The following object is masked from <U+393C><U+3E31>package:base<U+393C><U+3E32>:
pretty
Loading required package: GISTools
Loading required package: maptools
Checking rgeos availability: TRUE
Loading required package: RColorBrewer
Loading required package: MASS
Attaching package: <U+393C><U+3E31>MASS<U+393C><U+3E32>
The following object is masked from <U+393C><U+3E31>package:dplyr<U+393C><U+3E32>:
select
Loading required package: rgeos
rgeos version: 0.4-2, (SVN revision 581)
GEOS runtime version: 3.6.1-CAPI-1.10.1
Linking to sp version: 1.3-1
Polygon checking: TRUE
Loading required package: spatialEco
Loading required package: raster
Attaching package: <U+393C><U+3E31>raster<U+393C><U+3E32>
The following objects are masked from <U+393C><U+3E31>package:MASS<U+393C><U+3E32>:
area, select
The following object is masked from <U+393C><U+3E31>package:dplyr<U+393C><U+3E32>:
select
The following object is masked from <U+393C><U+3E31>package:tidyr<U+393C><U+3E32>:
extract
Shapefile Object with Spatial data Import data for past 12 years
Requires translation of chinese character independetly (https://stat.ethz.ch/pipermail/r-sig-geo/2009-March/005323.html)
Taiwan follows EPSG 3826 (http://spatialreference.org/ref/epsg/twd97-tm2-zone-121/)
taiwan_ts_map_sp <- readOGR(dsn = "data/TAIWAN_TOWNSHIP", layer = "TOWN_MOI_1071226", stringsAsFactors=TRUE)
OGR data source with driver: ESRI Shapefile
Source: "C:\Users\terence.tan.2015\Desktop\dangy\data\TAIWAN_TOWNSHIP", layer: "TOWN_MOI_1071226"
with 368 features
It has 7 fields
#taiwan <- readShapePoly("data/taiwan_data/COUNTY_MOI_1070516.shp")
#taiwan@proj4string<- CRS( "+init=epsg:3826 +proj=longlat +ellps=WGS84 +no_defs")
#taiwan.union <- aggregate(taiwan)
df_dengue <- jsonlite::fromJSON("data/dengue_case.json") %>%
filter(as.Date(Onset_day) >= "2016-01-01" & as.Date(Onset_day)< "2017-01-01")
# Check for NA values for coordinates
sum(is.na(df_dengue$Minimum_statistical_area_center_point_X))
[1] 0
sum(is.na(df_dengue$Minimum_statistical_area_center_point_Y))
[1] 0
df_dengue<- df_dengue[!is.na(df_dengue$Minimum_statistical_area_center_point_X),]
df_dengue<- df_dengue[!(df_dengue$Minimum_statistical_area_center_point_X == 'None'),]
# Type conversion
df_dengue[, c(10,11,19,23,24)] <- sapply(df_dengue[, c(10,11,19,23,24)], as.numeric)
# Transform into SF object
sf_dengue <- st_as_sf(df_dengue,
coords = c("Minimum_statistical_area_center_point_X",
"Minimum_statistical_area_center_point_Y"),
crs = "+init=epsg:3826 +proj=longlat +ellps=WGS84 +no_defs",na.fail=FALSE)
sf_dengue <- na.omit(sf_dengue)
sf_dengue <- as(sf_dengue, 'Spatial')
sp_dengue <- as(sp_dengue, 'SpatialPoints')
tmap_mode("view")
tmap mode set to interactive viewing
tm_shape(taiwan_ts_map_sp)+
tm_borders(col = "grey40",alpha=0.5)+
# prevent zoom too much
tm_view(alpha = 1, set.zoom.limits = c(7,21))+
tm_layout(basemaps = c('OpenStreetMap'))+
tm_shape(sp_dengue)+
tm_dots(col ="red",size = 0.01)
As of version 2.0, basemaps and basemaps.alpha have to be called from tm_view